Recently, The Frogger and I were watching X-Men: The Last Stand (aka X-Men 3: Mutants Doing Ridiculous Wire-Work Stunts), which should get you thinking about what mutant powers you would like to have. Unfortunately, I'd already thought this through in some detail (control of gravity, take a minute to think through the relativistic implications and tremble Homo sapiens). So, I had time to ponder grander thoughts, like how the hell do they get those mutant powers? Actually, if one pays attention (I find that a naked, blue, reptilian Rebecca Romijn helps one focus), one can infer a fair bit about X-Men genetics with only some vigorous bending of one's suspension of disbelief (provided that you are cool with ignoring the laws of physics).

SUPPRESSING THE X-GENEWhat We Know: The effects of a mutated X-gene can be suppressed by treatment with an antibody derived from the mutant child Leech.

How We Know: It's only the major plot device of X-Men: The Last Stand.

What This Means: Suppression of the X-gene's effect by a single antibody suggests that the X-gene exerts its effects through a single protein product. The general mutant effects of the X-gene are probably due to changes in expression level, not change in function, because reducing the amount of active X-gene product makes mutants normal. Specific powers may be related to differences in X-gene function. The suppressive effect of the "mutant cure" is should wear off over time as the antibody is depleted (e.g., "cured" Magneto rocking a chess-piece's world in the final shot of X-Men: The Last Stand). Leech probably does not have a mutant X-gene, because the antibody does not negate his own power.DISTRIBUTION OF MUTANT POWERSWhat We Know: Mutant powers are classified by strength from 1-5, with 5 being the strongest and the rarest. Frequency of a class decreases as the powers get stronger.

How We Know: In X-Men: The Last Stand, Callisto tells Magneto that Jean Grey/Dark Phoenix is a Class 5 mutant, stronger than any other she has ever sensed before. She also indicates that mutants above a Class 3 are rare. This implies that mutants become progressively more rare as they become more powerful.

What This Means: This means that the mutation effect size follows an exponential distribution (i.e., larger effects are much more rare than small effects). This is the same type of distribution that scientists expect for real mutations in real genes.

MUTATION RATEWhat We Know: Mutant powers are caused by mutations in the X-gene

How We Know: For starters, Stan Lee said so. This repeat this information is repeated in X2 to Iceman's family.

What This Means: In humans, the probability of mutation is on the order of 10-9 per base pair. Given a reasonable guesstimate of the size of the X-gene, we should expect no more than a few thousand mutants in the United States. The X-Men trilogy strongly implies that there are far more mutants than this estimate. Mutation rate, however, is variable across the genome. The ending of X2 implies that the rate of human evolution (likely meaning the amount of variation in the human population) has suddenly increased. The mutation rate of X-gene may be orders of magnitude higher than the rest of the genome, probably due to BPA, nuclear power, MSG, microwaves, vaccines, George W. Bush, the decline of the traditional family, global warming, FOX canceling Firefly, etc.INHERITANCEWhat We Know: Mutant powers are inherited from the father.

How We Know: In X2, Pyro tells Iceman's family that its the dad's fault their son is weird.

What This Means: Normally, we think of things only being inherited from the father when the gene is located on the Y-chromosome, as this is the only uniquely male DNA floating around. Females are XX and males are XY. If the X-gene were on the Y-chromosome, there should not be any female mutants. X-inactivation of the mother's X-chromosome would allow a daughter to inherit their mutant powers from their father, but the sons would inherit their mutant powers from their mothers (son's X-chromosome always comes from Mom).

Of all the things in the X-Men trilogy, this is what ruins my suspension of disbelief? I need to get out more.

Have you considered that since this is a mutation gene that is new, then there is no allele to suppress in most cases? Perhaps the fault is with the father because in this rare instance the Y chromosome has crossed with the X chromosome for the mutation. It could be an x-chrom addition from the Y or simply a crossing over from the Y in an non-functional area. But then, if it's riding in on the father's X then there would be no male xmen. Hmm... Maybe there is something in the male chemistry or habits that cause a chromosomal mutation, then. Combination of testosterone plus tendency to engage in more activities with high chemical exposure?

It could be a product of genetic imprinting, which means that its expression is determined by whether the female or the male parent hands a particular gene down, but that's impossible if it's X-linked (sex-linked) because in that case, there would be no male mutants.
The only case in which this would be possible is if all mutant males were a product of non-disjunction of the sex chromosomes from their father. This is statistically HIGHLY unlikely, and there would still be significantly more mutant females than males. In addition, all mutant males would be stuck with female secondary sex characteristics and would likely not be able to reproduce, which ruins the whole thing anyway.
So in summary, it is remotely possible, and I'm not even going to get into the bit about the single antibody "curing" mutation, that struck me as a bit ridiculous, mutations are so varied and can be so extensive, there would have to be a pretty ridiculous amount of pleiotropy involved.

Did you ever think of the most simple explanation? Like maybe mutants have the chromosone pattern of a hermaphrodite? Which is X X Y that would implicate that they could be male or female and still carry it from the father simple solution!! And yea blue chick and on x 3 when she becomes human laying naked on the floor ooh la la

There is actually this thing called epigenetic inheritance. Genes are silenced by the addition of methyl groups to C5 in cytosine and recruitment of metyl binding domain proteins (MBDPs). The thing is that differential silencing of genes by epigenetic modification occurs defferentially between chromasomes inherited from the father and the mother. The same deletion on chromosome 15 leads to different diseases depending on whether its on the paternal or maternal chromosome (Prader Wili Syndrome if its on the paternal and Angelmans if its on the maternal chromosome. This could be used to explain how the "X-gene" is passed down the paternal line; it could be present in the maternal line but silenced by imprinting.

This can also be used to explain(in a round about way) how the same mutant gene gives different powers to people, but I'm bored after writing that first bit. Have a good'un!!